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Mar. Drugs 2017, 15(7), 213; doi:10.3390/md15070213

Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea

1
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7, Nanhai Road, Qingdao 266071, China
2
Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 1, Wenhai Road, Qingdao 266071, China
3
Ocean University of China, 5, Yushan Road, Qingdao 266071, China
*
Authors to whom correspondence should be addressed.
Received: 8 June 2017 / Revised: 27 June 2017 / Accepted: 30 June 2017 / Published: 5 July 2017
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Abstract

Crustacea, particularly Decapoda, contains many economically important species, such as shrimps and crabs. Crustaceans exhibit enormous (nearly 500-fold) variability in genome size. However, limited genome resources are available for investigating these species. Exopalaemon carinicauda Holthuis, an economical caridean shrimp, is a potential ideal experimental animal for research on crustaceans. In this study, we performed low-coverage sequencing and de novo assembly of the E. carinicauda genome. The assembly covers more than 95% of coding regions. E. carinicauda possesses a large complex genome (5.73 Gb), with size twice higher than those of many decapod shrimps. As such, comparative genomic analyses were implied to investigate factors affecting genome size evolution of decapods. However, clues associated with genome duplication were not identified, and few horizontally transferred sequences were detected. Ultimately, the burst of transposable elements, especially retrotransposons, was determined as the major factor influencing genome expansion. A total of 2 Gb repeats were identified, and RTE-BovB, Jockey, Gypsy, and DIRS were the four major retrotransposons that significantly expanded. Both recent (Jockey and Gypsy) and ancestral (DIRS) originated retrotransposons responsible for the genome evolution. The E. carinicauda genome also exhibited potential for the genomic and experimental research of shrimps. View Full-Text
Keywords: Exopalaemon carinicauda Holthuis; genome; caridean shrimp; genome size evolution Exopalaemon carinicauda Holthuis; genome; caridean shrimp; genome size evolution
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Yuan, J.; Gao, Y.; Zhang, X.; Wei, J.; Liu, C.; Li, F.; Xiang, J. Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea. Mar. Drugs 2017, 15, 213.

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